Hello and thanks for your reply,
My sander inputfile looks like:
For steepest decent and conjugated gradient:
# Running minimization
cat << eof > min.in
# 20000 steps of minimization
&cntrl
maxcyc=20000, imin=1, ntmin=1, ntcyc=2000, cut=10.0, igb=1, ntb=0, ntpr=200,
/
For XMIN:
# Running minimization
cat << eof > min.in
# 1000 steps of minimization
&cntrl
maxcyc=1000, imin=1, ntmin=3, cut=10.0, igb=1, ntb=0, ntpr=200,
/
My input files are prepared by using antechamber and a mopin-file. The prmtop is prepared using tleap, frcmod using parmchk.
My input coord-file looks like
3rec_prep.mopin
63
0.0000000 0.0000000 0.0000000 1.4500000 0.0000000 0.0000000
2.1700000 0.0000000 1.2470000 1.4500000 0.0000000 2.4940000
0.0100000 0.0000000 2.4940000 -0.7100000 0.0000000 1.2470000
-1.9300000 0.0000000 1.2540000 -0.4940000 0.0000000 3.3670000
2.0600000 0.0000000 3.5510000 -0.4830000 0.0000000 -1.3670000
1.9940000 0.0000000 -0.9430000 -0.6040000 -1.0270000 -1.7090000
-0.7660000 0.6840000 -2.1660000 0.5250000 0.3420000 -1.5950000
3.5860000 0.0000000 1.5100000 4.0610000 -1.3670000 1.5990000
5.4870000 -1.3670000 1.8630000 5.9620000 0.0000000 1.9520000
4.8910000 0.8800000 1.7530000 3.2790000 0.3420000 2.4980000
4.1990000 -1.7690000 0.5960000 3.6340000 -2.2380000 2.0940000
5.5550000 -1.7090000 0.8320000 6.0520000 -0.2280000 3.0130000
6.6780000 1.1290000 1.3900000 6.9960000 1.7930000 2.1920000
7.2790000 1.3180000 0.5020000 6.0300000 1.8730000 0.3970000
6.5960000 2.5800000 0.1100000 5.7370000 -2.0270000 3.0730000
5.9700000 -3.5850000 2.7920000 5.2560000 -4.4460000 3.9370000
4.9410000 -3.3390000 1.5910000 7.4730000 -3.2560000 3.2300000
3.8840000 -4.1720000 3.9390000 3.2050000 -5.0940000 3.0490000
3.4920000 -4.2890000 4.9490000 3.4230000 -3.3050000 3.4690000
2.8070000 -6.2760000 3.7880000 1.3660000 -6.4230000 3.7260000
0.8030000 -5.3380000 2.9450000 1.8330000 -4.4990000 2.5020000
3.3990000 -5.3630000 2.0120000 2.6130000 -6.0070000 4.8260000
3.0040000 -7.6590000 3.6940000 3.9350000 -7.8480000 3.7140000
0.9540000 -6.3950000 4.7340000 0.9730000 -7.2890000 3.1970000
0.1100000 -4.7680000 3.5610000 0.1030000 -5.8790000 1.8090000
-1.2720000 -6.1220000 2.1640000 -1.9720000 -6.6630000 1.0280000
-1.0650000 -6.7790000 -0.0850000 0.2490000 -6.3140000 0.3130000
-1.4800000 -5.8490000 3.1970000 -1.0280000 -7.2080000 -1.4700000
0.2010000 -7.1260000 -2.2160000 1.3930000 -6.6180000 -1.5870000
1.3560000 -6.1930000 -0.2120000 2.3220000 -6.5560000 -2.1510000
-2.2200000 -7.7150000 -2.0980000 -2.9810000 -7.7020000 -1.4370000
-2.5480000 -8.0780000 -2.9800000
only 63-atoms.
Using steepest decent i will get a LINMIN error, using XMIN i will get this error: ERROR in load_lbfgs(): YS=0
Best regards
Jan Wahl
-------- Original-Nachricht --------
> Datum: Tue, 11 Jan 2011 14:15:49 -0500
> Von: Jason Swails <jason.swails.gmail.com>
> An: AMBER Mailing List <amber.ambermd.org>
> Betreff: Re: [AMBER] LINMIN FAILURE using amber 11
> You're running in vacuum? What do your input files look like? How many
> atoms are in your system?
>
> On Tue, Jan 11, 2011 at 2:05 PM, Jan Wahl <JanWahl.gmx.de> wrote:
>
> > Hi Ben,
> > thanks for your reply. I#m not usin g any solvat model so it has to be
> an
> > xmin error.
> >
> > But thanks a lot anyway
> >
> >
> > Jan
> >
> >
> > -------- Original-Nachricht --------
> > > Datum: Tue, 11 Jan 2011 11:38:32 -0500
> > > Von: Ben Roberts <ben.roberts.geek.nz>
> > > An: AMBER Mailing List <amber.ambermd.org>
> > > Betreff: Re: [AMBER] LINMIN FAILURE using amber 11
> >
> > > Hi Jan,
> > >
> > > On 11/1/2011, at 10:22 a.m., Jan Wahl wrote:
> > >
> > > > Thank you very much for your help.
> > > >
> > > > I'm going to try to use XMIN instead of the standard minimizer but i
> > > will get now an error
> > > >
> > > >
> > > > ERROR in load_lbfgs(): YS=0
> > > >
> > > >
> > > > some ideas???
> > >
> > > I've used XMIN before and have received this error. It's common with
> > > explicit solvent. You're likely to struggle with XMIN unless you
> either
> > (a)
> > > freeze all or most solvent molecules, or (b) minimise using implicit
> > solvent
> > > (Generalised Born or Poisson-Boltzmann).
> > >
> > > Hope that helps,
> > >
> > > Ben
> > >
> > > --
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> > >
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>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
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Received on Wed Jan 12 2011 - 01:30:02 PST
